Variant report

Variant	rs3781197
Chromosome Location	chr10:90042774-90042775
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10509540	0.82[ASN][1000 genomes]
rs12415812	0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs12416116	0.88[ASN][1000 genomes]
rs166976	0.83[ASN][1000 genomes]
rs17110523	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2018705	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs286487	0.85[ASN][1000 genomes]
rs3781196	0.87[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45585838	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs558443	0.90[EUR][1000 genomes]
rs60888743	0.88[ASN][1000 genomes]
rs7068821	0.88[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7094781	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs737391	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7922058	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9665166	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs999951	0.82[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895879	chr10:90015725-90219298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3781197	LIPJ	cis	cerebellum	SCAN
rs3781197	CH25H	cis	cerebellum	SCAN
rs3781197	PCGF5	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90037800-90043200	Enhancers	Dnd41	blood
2	chr10:90038600-90042800	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr10:90038800-90043000	Enhancers	Fetal Thymus	thymus
4	chr10:90039000-90043000	Enhancers	Primary hematopoietic stem cells	blood
5	chr10:90039200-90042800	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr10:90039800-90042800	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr10:90039800-90043000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr10:90039800-90043000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr10:90040600-90042800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:90040600-90042800	Enhancers	HMEC	breast
11	chr10:90041000-90042800	Enhancers	Thymus	Thymus
12	chr10:90041000-90042800	Enhancers	Hela-S3	cervix
13	chr10:90041200-90042800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr10:90041200-90043200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr10:90041400-90042800	Flanking Active TSS	Osteobl	bone
16	chr10:90041400-90043000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr10:90041600-90042800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr10:90041600-90042800	Enhancers	Primary B cells from peripheral blood	blood
19	chr10:90041600-90042800	Enhancers	Primary T cells from cord blood	blood
20	chr10:90041600-90042800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr10:90041600-90042800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr10:90041600-90042800	Enhancers	HSMM	muscle
23	chr10:90041600-90042800	Flanking Active TSS	NHDF-Ad	bronchial
24	chr10:90041600-90042800	Enhancers	NHEK	skin
25	chr10:90041600-90043000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr10:90041600-90043000	Enhancers	Fetal Lung	lung
27	chr10:90041800-90042800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:90041800-90042800	Flanking Active TSS	NHLF	lung
29	chr10:90042000-90042800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr10:90042000-90042800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr10:90042000-90042800	Enhancers	Fetal Stomach	stomach
32	chr10:90042000-90042800	Enhancers	Left Ventricle	heart
33	chr10:90042000-90042800	Enhancers	Psoas Muscle	Psoas
34	chr10:90042000-90043000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr10:90042200-90042800	Enhancers	Ovary	ovary
36	chr10:90042200-90042800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr10:90042200-90043000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr10:90042200-90043000	Enhancers	Adipose Nuclei	Adipose
39	chr10:90042200-90043800	Weak transcription	GM12878-XiMat	blood
40	chr10:90042200-90048400	Weak transcription	Pancreas	Pancrea
41	chr10:90042400-90042800	Enhancers	Placenta Amnion	Placenta Amnion
42	chr10:90042400-90042800	Enhancers	Sigmoid Colon	Sigmoid Colon
43	chr10:90042400-90042800	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr10:90042400-90043000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr10:90042400-90043000	Enhancers	Fetal Muscle Leg	muscle
46	chr10:90042400-90043000	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr10:90042400-90043000	Enhancers	Right Atrium	heart
48	chr10:90042400-90043000	Enhancers	NH-A	brain
49	chr10:90042400-90043200	Enhancers	Muscle Satellite Cultured Cells	--
50	chr10:90042400-90043200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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